SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Andrew J. Page, Ben Taylor, Aidan Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris

Research output: Contribution to journalArticlepeer-review


Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
Original languageEnglish
JournalMicrobial Genomics
Publication statusPublished - 20 Mar 2016

Bibliographical note

This is an open access article published by the Microbiology Society under the Creative Commons Attribution-NonCommercial License


Dive into the research topics of 'SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments'. Together they form a unique fingerprint.

Cite this